Structural biology articles within Nature Methods

Featured

  • Technology Feature |

    Chemical modifications to DNA, histones and RNA make changes happen. Scientists are exploring ways to track these modifications and how they interact.

    • Vivien Marx

  • Editorial |

    The COVID-19 pandemic has highlighted the importance of methodological advancements in basic biological research. We believe that method development will continue to propel both fundamental and applied studies on SARS-CoV-2 and other pathogens.

  • Method to Watch |

    Emerging algorithms are extracting information about macromolecular motions from cryo-EM data.

    • Allison Doerr

  • Research Highlights |

    DNA and chromatin structures can be visualized in situ with electron tomography.

    • Zachary J Lapin

  • Research Highlights |

    A serial-section electron microscopy data set of larval zebrafish brain—imaged at several scales—provides a resource for structure–function analyses of the animals' neural circuitry.

    • Nina Vogt

  • Research Highlights |

    Low-energy holography enables imaging single proteins and protein complexes.

    • Zachary J Lapin

  • Research Highlights |

    A rapid mix-and-inject serial femtosecond crystallography approach enables structure determination of ligand-binding intermediates.

    • Allison Doerr

  • Editorial |

    The end of 'blob-ology': single-particle cryo-electron microscopy (cryo-EM) is now being used to solve macromolecular structures at high resolution.

  • Research Highlights |

    Researchers study the structure of the metalloenzyme photosystem II by applying femtosecond X-ray pulses to simultaneously record X-ray diffraction and X-ray emission spectroscopy data.

    • Allison Doerr

  • Resource |

    Interactome3D is an interactive resource allowing biologists to use available structural information to model protein-protein interactions and structurally annotate protein interaction networks.

    • Roberto Mosca
    • , Arnaud Céol
    •  & Patrick Aloy

  • News & Views |

    A new toolbox for structural biology that combines single-molecule fluorescence and molecular modeling is used to generate high-precision structures of protein complexes.

    • Timothy D Craggs
    •  & Achillefs N Kapanidis

  • Article |

    A collection of simulation tools and workflow for single-molecule Förster resonance energy transfer (smFRET) allows highly quantitative structural modeling. This hybrid approach yields a model of reverse-transcriptase binding to DNA at sub-angstrom accuracy when benchmarked against a crystal structure and can resolve a flexible single-stranded template overhang.

    • Stanislav Kalinin
    • , Thomas Peulen
    •  & Claus A M Seidel

  • News & Views |

    Researchers adapt a popular Orbitrap-based mass spectrometer to detect and analyze large, intact protein complexes, accelerating a new frontier in structural biology.

    • Philip D Compton
    •  & Neil L Kelleher

  • Brief Communication |

    Removing phosphopantetheine-tagged labels from acyl carrier proteins (ACPs) and ACP fusion proteins contributes to a versatile labeling method in which tags can be iteratively swapped.

    • Nicolas M Kosa
    • , Robert W Haushalter
    •  & Michael D Burkart

  • Brief Communication |

    Lipidic sponge phase crystallization yields membrane protein microcrystals that can be injected into an X-ray free electron laser beam, yielding diffraction patterns that can be processed to recover the crystal structure.

    • Linda C Johansson
    • , David Arnlund
    •  & Richard Neutze

  • Brief Communication |

    The use of dual-objective detection with astigmatism-based three-dimensional stochastic optical reconstruction microscopy (STORM) imaging improves resolution more than twofold and removes noise in resulting super-resolution images. This allowed detailed fluorescence imaging of distinctive features of the three-dimensional actin cytoskeleton ultrastructure with single-filament resolution in cells.

    • Ke Xu
    • , Hazen P Babcock
    •  & Xiaowei Zhuang

  • Research Highlights |

    Molecularly imprinted polymers act as 'smart' nucleants for protein crystallization.

    • Petya V Krasteva

  • Article |

    Three-dimensional structural RNA modules, defined as ensembles of stacked arrays of ordered non-Watson-Crick base pairs, are found in many RNAs and play important functional roles. The presented computational tool, RMDetect, allows the identification of common RNA modules from sequence alone.

    • José Almeida Cruz
    •  & Eric Westhof

  • Brief Communication |

    A microfluidic mixing device for multiple, rapid and automated single-molecule measurements permits the study of macromolecule properties under varying environmental conditions. Also in this issue, Gambin et al. present another microfluidic mixing device for rapid single-molecule measurements.

    • Soohong Kim
    • , Aaron M Streets
    •  & Devdoot S Majumdar

  • This Month |

    Fluorescent proteins can be located in electron micrographs.

    • Monya Baker
    •  & Erik Jorgensen

  • Article |

    Methods are reported for the combination of fluorescence nanoscopy using either stimulated emission depletion microscopy (STED) or photoactivated localization microscopy (PALM) with electron microscopy, to achieve correlative imaging in which the super-resolved fluorescence signal is placed in the context of cellular ultrastructure.

    • Shigeki Watanabe
    • , Annedore Punge
    •  & Erik M Jorgensen

  • Research Highlights |

    Researchers determined the excited-state structure of a small protein using nuclear magnetic resonance spectroscopy.

    • Allison Doerr

  • Article |

    Single-molecule fluorescence resonance energy transfer (FRET) is a useful technique for monitoring biomolecular dynamics. A new method, termed switchable FRET, facilitates monitoring of multiple distances in single molecules, using a single donor and multiple spectrally identical acceptors that are switched on and off between a fluorescent state and a dark state.

    • Stephan Uphoff
    • , Seamus J Holden
    •  & Achillefs N Kapanidis

  • Research Highlights |

    Researchers solve a high-resolution structure of a seven-helix transmembrane protein using nuclear magnetic resonance (NMR) spectroscopy.

    • Allison Doerr

  • Brief Communication |

    Single-molecule fluorescence resonance energy transfer (smFRET) is applied in live cells and reveals the conformational changes of individual SNARE proteins upon entering a SNARE complex.

    • John J Sakon
    •  & Keith R Weninger

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